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MicrobeTracker specifications


Unique identifier OMICS_26046
Name MicrobeTracker
Alternative name MicrobeTracker Suite
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Registration required Yes
Maintained Yes




No version available


  • person_outline Christine Jacobs-Wagner
  • person_outline Thierry Emonet

Publication for MicrobeTracker

MicrobeTracker citations


The cell wall hydrolase Pmp23 is important for assembly and stability of the division ring in Streptococcus pneumoniae

Sci Rep
PMCID: 5954120
PMID: 29765094
DOI: 10.1038/s41598-018-25882-y

[…] mouse IgG in PBS-Triton-BSA. Following washing, slides were mounted with 5% (wt/vol) polyvinyl alcohol.Images were acquired using the Volocity software package. Image analysis was performed using the MicrobeTracker Matlab software. Distributions of cell dimensions among cell populations were represented with box plots displaying the interquartile range (25th and 75th percentiles), the median value […]


The transcription repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage

Nat Commun
PMCID: 5910403
PMID: 29679003
DOI: 10.1038/s41467-018-03790-z

[…] ingleMolecule/smb-plugins). Raw videos (nd2 format) were converted into TIF files using Bio-Formats plugin, flattened with excitation beam profile as described previously. Cell outlines were drawn in MicrobeTracker. For quantification of binding events, peaks were detected in the reactivation phase (Fig. : frames 31−50, Fig. : frames 51−100, Table  and Fig. : frames 101−200). Peaks were detected b […]


DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli

PLoS Genet
PMCID: 5792023
PMID: 29351274
DOI: 10.1371/journal.pgen.1007161

[…] We selected regions of images occupied by cells to obtain information about pol IV upregulation upon ciprofloxacin treatment (>200 cells; all 5 min frames during the 3h experiment). MicrobeTracker 0.937 [], a MATLAB script, was used to create cell outlines as regions of interest (ROI). We manually curated cell outlines designated by MicrobeTracker to ensure accuracy and to ensure […]


MukB ATPases are regulated independently by the N and C terminal domains of MukF kleisin

PMCID: 5812716
PMID: 29323635
DOI: 10.7554/eLife.31522.039

[…] cells from1 ml of culture were taken, centrifuged, placed on agarose pad and imaged. As a control, strain carrying empty pBAD24 vector was analysed. Cells were segmented from brightfield images using MicrobeTracker (). MukB foci were detected using ‘spotfinderM’, available as part of the MicrobeTracker Suite. […]


Communication across the bacterial cell envelope depends on the size of the periplasm

PLoS Biol
PMCID: 5736177
PMID: 29257832
DOI: 10.1371/journal.pbio.2004303
call_split See protocol

[…] phase-contrast objective (Plan-Achromat 40×/0.65 Ph2; Carl Zeiss). Images were acquired with Zen 2 (blue edition; Carl Zeiss). Exposure times and image scaling were identical for compared conditions. MicrobeTracker [] was used to obtain cell outlines. Quantitative analysis from cell meshes was done with MATLAB R2014a (Mathworks, Inc.) using custom scripts to plot the distributions of length-to-wid […]


Permissive zones for the centromere binding protein ParB on the Caulobacter crescentus chromosome

Nucleic Acids Res
PMCID: 5815017
PMID: 29186514
DOI: 10.1093/nar/gkx1192

[…] in the presence of appropriate antibiotics before being spotted to agarose pad for microscopy observation. Phase contrast (150 ms exposure) and fluorescence images (1000 ms exposure) were collected. MicrobeTracker (http://microtracker.org) was used to detect cell outlines and cell length (). SpotFinderM was used to manually detect fluorescent foci positions (). Data (cell length, foci number) wer […]


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MicrobeTracker institution(s)
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT, USA; Department of Physics, Yale University, New Haven, CT, USA; Section of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
MicrobeTracker funding source(s)
Supported by the National Institutes of Health (GM076698 and GM065835), and the National Science Foundation (CCF-0829836).

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